More than two decades have passed since the first studies documenting genetic population structure of green turtles (Chelonia mydas) were published. Since then many more have followed and characterization of the genetic structure of green turtle rookeries now covers most of the global distribution of the species, benefitting conservation of this threatened species worldwide. However, important data gaps still exist across a large part of the western and central Pacific Ocean (WCPO). This large area is made up of hundreds of scattered islands and atolls of Micronesia, Melanesia, and Polynesia, most of which are remote and difficult to access. In this study, we assessed stock structure of green turtles throughout the WCPO using mitochondrial (mt) DNA from 805 turtles sampled across 25 nesting locations. We examined whether sequencing longer fragments (770 bp) of the control region increases resolution of stock structure and used genetic analysis to evaluate level of demographic connectivity among island nesting populations in the WCPO. We identified a total of 25 haplotypes characterized by polymorphism within the 770 bp sequences, including five new variants of haplotypes that were indistinguishable with shorter 384 bp reads from previous studies. Stock structure analysis indicated that rookeries separated by more than 1,000 km were significantly differentiated from each other, but neighboring rookeries within 500 km showed no genetic differentiation. Results presented in this paper establish that sequencing of longer fragments (770 bp) of the control region does in some cases increase resolution and that there are at least seven independent stocks in the region.